Preheat oven to 300 degrees F.
Combine cracker crumbs and melted butter. Divide crumbs among mini muffin tins that have been sprayed with a nonstick cooking spray. Saute onion for 10 minutes in 2 tablespoons butter. Cool, then divide evenly on top of cracker crumbs. Beat eggs; add milk, salt, pepper, and Swiss cheese. Pour by spoonfuls on top of onions in tins. Do not fill to top, as they will run over. Bake until set, about 15 to 20 minutes. Do not over bake. May be stored in refrigerator or freezer. Warm in oven before serving.
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